GEO DataSets

(Submitter supplied) Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

5 Samples

Download data: CSV

(Submitter supplied) The association of genomic loci to the nuclear periphery is proposed to facilitate cell type-specific gene repression and influence cell fate decisions. However, the interplay between gene position and expression remains incompletely understood, in part because the proteins that position genomic loci at the nuclear periphery remain unidentified. Here, we used an Oligopaint-based HiDRO screen targeting ∼1000 genes to discover novel regulators of nuclear architecture in Drosophila cells.We identified the heterochromatin-associated protein Stonewall (Stwl) as a factor promoting perinuclear chromatin positioning. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25244 GPL19132

37 Samples

Download data: BED, BW

(Submitter supplied) Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in Genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

24 Samples

Download data: BED, BW

(Submitter supplied) Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

8 Samples

Download data: CSV

(Submitter supplied) Abstract: During Drosophila oogenesis, germline stem cell (GSC) identity is maintained largely by preventing the expression of factors that promote differentiation. This is accomplished via the activity of several genes acting either in the GSC or its niche. The translational repressors, Nanos and Pumilio, act in GSCs to prevent differentiation, likely by inhibiting translation of early differentiation factors, while niche signals prevent differentiation by silencing transcription of the differentiation factor Bam. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Dataset:

GDS2734

Platform:

GPL1322

6 Samples

Download data: CEL

Comparison of ovaries from bag of marbles (bam) mutants and stonewall (stwl) bam double mutants. Stwl is a DNA-associated protein required for germline stem cell (GSC) maintenance; Bam is a key differentiation factor. Results provide insight into the role of Stwl in maintaining germ cell identity.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1322

Series:

GSE6928

6 Samples

Download data: CEL

(Submitter supplied) The maintenance and differentiation of highly potent animal stem cells generates an epigenetic cycle that underlies development. Drosophila female germline stem cells (GSC) produce cystoblast daughters that differentiate into nurse cells and oocytes. Developmental chromatin analysis profiling the differentiation of GSCs into cystoblasts and NCs of increasing ploidy shows that cystoblasts start developing by forming heterochromatin while in a transient syncytial state, the germline cyst, reminiscent of early embryonic cells. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL19132

28 Samples

Download data: BEDGRAPH, BW, CSV, TXT

(Submitter supplied) Germline stem cell self-renewal and differentiation are required for sustained production of gamates. GSC differentiation in drosophila requires expression of setdb1 by the somatic niche, however its function is not known. We used microarray analysis to determine what genes does setdb1 regulate to affect differentiation.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

6 Samples

Download data: CEL, CHP

(Submitter supplied) In a broad range of organisms, Piwi-interacting RNAs (piRNAs) have emerged as core components of a surveillance system that protects the genome by silencing transposable and repetitive elements. A vast proportion of piRNAs is produced from discrete genomic loci, termed piRNA clusters. The molecular mechanisms and the factors that govern the expression of these loci are largely unknown. We have preciously shown the Cutoff (Cuff), a protein with similarity to yeast Rai1, is a component of the piRNA pathway. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

4 Samples

Download data: WIG

(Submitter supplied) Purpose: Piwi family protein Aubergine (Aub) maintains genome integrity in late germ cells of the Drosophila ovary through piRNA-mediated repression of transposon activities. Although it is highly expressed in germline stem cells (GSCs) and early progeny, it remains unclear if it plays any roles in early GSC lineage development. Results: The study reveals a novel function of Aub in GSCs and their progeny, which promotes translation of self-renewal and differentiation factors by directly binding to its target mRNAs and interacting with translational initiation factors.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL17275

3 Samples

Download data: BED

(Submitter supplied) LEM Domain proteins are key components of the nuclear lamina. Mutations in LEM-D proteins cause dystrophic diseases associated with compromised adult stem cells, yet it remains unclear how LEM-D proteins support stem cell function. Studies described here use the homologue of the LEM-D protein emerin in Drosophila, Otefin (Ote) as a model to understand LEM-D protein function in adult stem cells. Loss of Ote causes female sterility due to a complex germline stem cell (GSC) phenotype that includes both an early block in germline differentiation followed by GSC death. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

8 Samples

Download data: CEL

(Submitter supplied) Here we used laser cutting microdissection and RNA amplification to profile the gene expression in wildtype female germaria and male apex of the testes. These tissue contain germline stem cells and early dividing germ cells. Our goal was to identify genes expressed in these cell types.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL3880

4 Samples

Download data: GPR

(Submitter supplied) The piRNA-interacting Piwi protein is involved in transcriptional silencing of transposable elements in ovaries of D. melanogaster. Here we characterized the genome-wide effect of nuclear Piwi elimination on the presence of the heterochromatic H3K9me3 mark and HP1a, as well as on the transcription-associated mark H3K4me2. Our results demonstrate that a significant increase in the H3K4me2 level upon nuclear Piwi loss is not accompanied by the alterations in H3K9me3 and HP1a levels for several germline-expressed transposons, suggesting that in this case Piwi prevents transcription by a mechanism distinct from H3K9 methylation. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

16 Samples

Download data: BEDGRAPH

(Submitter supplied) rasiRNA (rasiRNAs, repeat-associated short interfering RNAs) system is a mechanism of silencing of mobile element transpositions in germline of a number of species including Drosophila melanogaster. rasiRNA itself is a short RNAs which participate in transposon transcription repression and mRNA degradation. Defects in rasiRNA system lead to increased transposition rate and developmental abnormalities due to accumulation of double-strand DNA breaks in fruitfly testes and ovaries. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL3603

6 Samples

Download data: GPR

(Submitter supplied) During early Drosophila embryogenesis, the essential pioneer factor Zelda defines hundreds of cis-regulatory regions and in doing so reprograms the zygotic transcriptome. While Zelda is essential later in development, it is unclear how the ability of Zelda to define cis-regulatory regions is shaped by cell-type specific chromatin architecture established during differentiation. Asymmetric division of neural stem cells (neuroblasts) in the fly brain provide an excellent paradigm for investigating the cell-type specific functions of this pioneer factor. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244

21 Samples

Download data: BED, BW

(Submitter supplied) Drosophila ovarian germline stem cells (GSCs) are a powerful model for stem cell research. However, due to the scarcity of GSCs in ovarian tissue, it is difficult to obtain the transcriptional profile of GSCs and identify novel GSC markers. In this study, we took advantage of single cell RNA sequencing (scRNA-seq) to profile the germline cells and somatic cells in wild type Drosophila ovary. We then performed an in vivo RNAi screen and network analysis to identify genes that are involved in the early stages of germ cell differentiation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

1 Sample

Download data: MTX, TSV

(Submitter supplied) Comparison of wild type and tumorous ovaries reveals that tumors inappropriately express a large number of testis genes

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: TXT

(Submitter supplied) Background. Telomeric small RNAs related to PIWI-interacting RNAs (piRNAs) have been described in various eukaryotes; however, their role in germline-specific telomere function remains poorly understood. Using a Drosophila model, we performed an in-depth study of the biogenesis of telomeric piRNAs and their function in telomere homeostasis in the germline. Results To fully characterize telomeric piRNA clusters, we integrated the data obtained from analysis of endogenous telomeric repeats, as well as transgenes inserted into different telomeric and subtelomeric regions. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13304 GPL17275

9 Samples

Download data: TXT

(Submitter supplied) With the ChIP-seq experiment, we identified direct target genes of E(Pc) specifically in somatic gonadal cells. We found that the E(Pc)-binding genes are enriched with signaling pathway components, consistent with our functional data showing prevailing germline defects even when E(Pc) function is exclusively compromised in somatic gonadal cells. In addition, we also performed RNA-seq to compare transcriptomes between E(Pc) knockdown testes and control testes.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL16479 GPL17275

8 Samples

Download data: BEDGRAPH, TXT